A Sky spokeswoman said Mr Murdoch was "uniquely well-placed" to be chairman.
Martin Gilbert, the deputy chair, said the board had looked at the Fox takeover in the best interests of shareholders and had impartial discussions that did not include Murdoch or other Sky directors with connections to Fox.
Later on Thursday, shareholders voted in favour of the re-election of Murdoch´s son James as chairman.
Fox owns 39.1% of Sky is trying to purchase the entire company in a deal worth $18.5 billion.
One significant hindrance to Fox's $15 billion bid has been the spate of sex-abuse and harassment scandals at Fox News, from the disgraced late founder Roger Ailes to onetime ratings powerhouse Bill O'Reilly, who was ousted by the network earlier this year.
Despite their position, Murdoch's level of support actually increased from 47% previous year, and the votes attached to Fox's 39% shareholding in Sky meant that both his reappointment and the remuneration report were approved comfortably overall.
In a stock exchange announcement detailing the AGM vote, Sky said: "The board is pleased that the majority of resolutions have been passed with a high level of support from shareholders".
Earlier this year, the deal was referred by Karen Bradley, the secretary of state for culture, media and sport, to the Competition and Markets Authority (CMA) on the grounds of concerns about media plurality and broadcasting standards.
He told shareholders he was "pretty confident" that this would not have an effect on the CMA's investigation.
"Independent oversight of the board is particularly important given Fox's ongoing bid to acquire Sky".
A United Kingdom investigation into a planned takeover of TV giant Sky by Rupert Murdoch's 21st Century Fox will assess the tycoon's influence on the country's political landscape, regulators said Tuesday.
Like-for-like revenues were up five per cent to £3.3bn in the three months to 30 September, from £3.1bn this time previous year.
"We've had a strong start to our new financial year with good revenue growth and excellent profit growth as investments we've made come through", said group chief executive Jeremy Darroch.
He said the first series of Sky's home-grown drama Riviera achieved 20 million downloads, while Game of Thrones had become the most watched series ever on Sky. The pay package handed to Sky's chief executive, Jeremy Darroch, quadrupled to more than £16m in the year to the end of June, despite a hefty fall in annual profits at the broadcaster's United Kingdom and Ireland business.
Shares in 21st Century Fox were flat at $25.50 in light-volume trading.